Variant report

Variant	rs58449189
Chromosome Location	chr2:38993552-38993553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr2:38993422-38993570	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38992665..38995431-chr2:39003330..39006208,3	K562	blood:
2	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
3	chr2:38992046..38994768-chr2:39003878..39006153,3	MCF-7	breast:
4	chr2:38993209..38995928-chr2:39007575..39009225,2	MCF-7	breast:
5	chr2:38989424..38992394-chr2:38992856..38995438,2	K562	blood:
6	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
7	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:
8	chr2:38991817..38994202-chr2:39346658..39349506,2	MCF-7	breast:
9	chr2:38992289..38994375-chr2:38996037..38998957,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000232114	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000115904	Chromatin interaction
ENSG00000232114	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000227238	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11888905	1.00[AMR][1000 genomes]
rs11892292	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11894209	1.00[AMR][1000 genomes]
rs11899756	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4592827	1.00[AMR][1000 genomes]
rs55809581	1.00[AMR][1000 genomes]
rs56239346	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56407729	1.00[AMR][1000 genomes]
rs58080550	1.00[AMR][1000 genomes]
rs59364009	1.00[AMR][1000 genomes]
rs60895887	1.00[AMR][1000 genomes]
rs61139307	1.00[AMR][1000 genomes]
rs61556896	1.00[AMR][1000 genomes]
rs6708518	1.00[AMR][1000 genomes]
rs6724203	1.00[AMR][1000 genomes]
rs6756998	1.00[AMR][1000 genomes]
rs73930361	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73930365	1.00[AMR][1000 genomes]
rs73930366	1.00[AMR][1000 genomes]
rs73930371	1.00[AMR][1000 genomes]
rs73930376	1.00[AMR][1000 genomes]
rs73930385	1.00[AMR][1000 genomes]
rs73930386	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:38991200-38994200	Weak transcription	HepG2	liver
3	chr2:38991800-38993600	Enhancers	Osteobl	bone
4	chr2:38991800-38993800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:38991800-38994400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:38992200-38995200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:38992800-38994200	Weak transcription	Fetal Heart	heart
8	chr2:38993200-38994200	Weak transcription	Liver	Liver
9	chr2:38993200-38994200	Weak transcription	HMEC	breast
10	chr2:38993200-38994400	Enhancers	NHEK	skin
11	chr2:38993200-38994600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:38993200-38994600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:38993400-38993800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:38993400-38998800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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